X-GEN

NAME

X-GEN - makemu

SYNOPSIS

makemu
[-afimnptvxyz] [-cval] [-sval] [rescut]

DESCRIPTION

"makemu" reads a merged data set (MULTIREF file) and a scaling
parameter file (SCALEIN) and uses it to generate several ASCII
files containing the merged intensities or structure amplitudes.
After writing the data out it also performs an analysis of the
Bijvoet differences in the data: it computes an overall scale and
relative temperature factor relating the primary observations
(F+ or I+) to the Bijvoet observations (F- or I-) and an R-factor
between the two sets. A large value of this "Bijvoet R" factor
might indicate the presence of a significant anomalous signal in
a data set, assuming adequate redundancy and a small overall error.

The "native" output format is the MULIST, whose format is described below.

Each line in the MULIST will contain either

h

k l I sig(I) I+ sig(I+) I- sig(I-) flag

or

h

k l F sig(F) F+ sig(F+) F- sig(F-) flag

where

I+ is the mean intensity of observations of the primary
reflection and its symmetry mates;
I- is the mean intensity for the Bijvoets;
F+ and F- are the corresponding structure amplitudes; and
sig(I), sig(I+ ), sig(I- ), sig(F), sig(F+ ), sig(F- ) are the
standard deviations associated with I, I+ , I- , F, F+ , and F- ,
respectively.

The flag value ranges from 0 to 63 and is the ORing of these conditions:

bit no.

condition for off condition for on

-------------------------------------------

0

acentric reflection centric reflection

1

I+ measurement made no I+ measurement

2

I- measurement made no I- measurement

3

mean intensity > 0 mean I <= 0

4

mean I+ > 0 mean I- <= 0

5

mean I- > 0 mean I- <= 0

Thus the possible values of the flag are:

flag

centricity <I> <I+> <I-> value

value

value value

0

acentric > 0 measured and <= 0 measured and > 0

1

centric > 0

2

acentric > 0 measured and > 0 not measured

4

acentric > 0 not measured measured and ? 0

9

centric < 0

16

acentric > 0 measured and < 0 measured and ? 0

24

acentric <= 0 measured and < 0 measured and ? 0

28

acentric <= 0 measured and < 0 not measured

32

acentric > 0 measured and ? 0 measured and < 0

40

acentric <= 0 measured and < 0 measured and > 0

42

acentric <= 0 not measured measured and < 0

56

acentric <= 0 measured and < 0 measured and < 0

The program also writes out data in five other ASCII formats to
separate files, whose names and environment variables are given
in the FILES section, below. The formats besides the MULIST are:

1. the "HKL" format used by XPREP and the various incarnations of

SHELX, consisting of (h,k,l,I,sigma(I),1), or (h,k,l,F,sigma(F),1)
formatted as follows:

0

2 5 249.17 6.97 1

2. a format intended as input to CNS, containing a six-line header

followed by reflection lines that look like

INDEx=

0 2 5 IOBS= 249.17 SIGI= 6.97

3. a format intended for XPLOR V.3.1, with no header and data lines

that look like

INDEx

0 2 5 IOBS 249.17 SIGMa 6.97

4. a format compatible with the /output.sca/ file put out by

SCALEPACK, with the Friedel-mates merged.

5. a format compatible with the /output.sca/ file put out by

SCALEPACK, with the Friedel-mates unmerged.

OPTIONS

-a

Output the ASCII MULIST (and the other ASCII output files)
in absolute hkl order rather than in standard X-GEN order. Thus in
a monoclinic spacegroup (0,2,3) will precede (2,0,3), and in
triclinic, monoclinic, or trigonal spacegroups (1,3,-7) will
precede (1,3,2).

-f

This specifies that structure amplitudes ("F's") will be

written out rather than intensities. Note that the resulting
square roots are taken separately for I, I+, and I-, so in general
<F> will not equal 0.5 * (<F+> + <F->). Note that for this option,
reflections with negative <I> will be output with <F> set to zero
and sigma(<F>) set to 9999.

-i

Reindex the reflections by a 3x4 matrix transformation on

the indices before output. The transformation matrix is specified
in a file with environment variable REINDEX. If the matrix is
specified as
1 0 0 -1
0 -1 0 0
0 0 -1 0

even if we are outputting intensities rather than structure
amplitudes. This option is not recommended, but it is included
for those who want it.

-p

Ordinarily "makemu" corrects for any alteration in the

overall sin(theta) dependence of the data that the scaling
introduces. If this flag is on, this correction is NOT
performed, and the sin(theta) dependence of the scaled
data is preserved in the output.

-t

Write out the reflection lists in increasing order of

sin(theta) rather than in some hkl-based order.

-v

Ordinarily "makemu" determines sigma(<F>) or sigma(<I>)

according to a formula that is sensitive both to the variances of
the individual observations and to the deviations of those values
from their means. If this flag is set the program determines the
variance strictly from the variances of the inputs, namely
var(<I>) = 1. / (SUM (1. / var(Ii))

-x In the X-PLOR and CNS output files, write out the reflections

with the Friedel mates separated. This is the default behavior.

-y In the X-PLOR and CNS output files, write out the reflections

with the Friedel mates merged.

-c<val>

In the "Bijvoet R factor" calculations, use only the reflections
for which I/sigma is greater than <val>. Default value: 2.

-s<val>

This value specifies the overall scale factor to be
applied to the output F's or I's. Default value: 1.

<rescut>

specifies the high-resolution cutoff in Angstroms, above

which reflections will not be output. Default: no cutoff applied.

EXAMPLES

makemu

Output intensities (not amplitudes) with a scale
factor of 1 and using all the data:

makemu -ifps0.1

Output structure amplitudes with a scale factor of
0.1 and using data only to 1.7 A, changing to the
non-standard variance formula and reindexing the data
based on the contents of the REINDEX file: